RetrogeneDB ID: retro_mmus_280

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:85171519..85171810(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000062687
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Cks1b
• Ensembl ID: ENSMUSG00000028044
• Aliases: Cks1b, 2410005G18Rik, 2610005D03Rik, AA407784, Cks1, sid1334
• Description: CDC28 protein kinase 1b [Source:MGI Symbol;Acc:MGI:1889208]

Sequence

>retro_mmus_280
ATGCCGGCGTGCTGCTGGGAGTTGTCTGGAGGCCAGAGGCGCGGGGCAATCATGTCCCACAAACAAATCTATTATTCGGA
CAAATACGACGACGAGGAGTTCGAGTACCGGCATGTCATGTTGCCCAAGGACATAGACAAGTTGGTCCCTAAAACCCATT
TGATGTCTGAATCTGAATGGAGGAAGCTCGGCGTTCAGCAGAGTCAGGGATGGGTCCACTATATGATCCATGAACCAGAA
CTTCACATCTTACTGTTCCAGTGGCCACTGCCCAAGAAGCCAAAGAAATGA

Alignment

ORF - retro_mmus_280 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFR
          MSHKQIYYSDKYDDEEFEYRHVMLPKDI.KLVPKTHLMSESEWR.LGVQQSQGWVHYMIHEPE.HILLF.
Retrocopy MSHKQIYYSDKYDDEEFEYRHVMLPKDIDKLVPKTHLMSESEWRKLGVQQSQGWVHYMIHEPELHILLFQ

Parental  RPLPKKPKK
          .PLPKKPKK
Retrocopy WPLPKKPKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.98 RPM
SRP007412_cerebellum	0.00 RPM	1.00 RPM
SRP007412_heart	0.00 RPM	1.96 RPM
SRP007412_kidney	0.00 RPM	1.50 RPM
SRP007412_liver	0.00 RPM	2.62 RPM
SRP007412_testis	0.00 RPM	3.66 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_280 was not detected

EST

No EST(s) were mapped for retro_mmus_280 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_144909	445 libraries	302 libraries	239 libraries	79 libraries	7 libraries

The graphical summary, for retro_mmus_280 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_280 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033635	10 retrocopies	retro_cjac_13, retro_cjac_1441, retro_cjac_1478, retro_cjac_1779, retro_cjac_2040, retro_cjac_2212, retro_cjac_2649, retro_cjac_276, retro_cjac_57, retro_cjac_876,
Dipodomys ordii	ENSDORG00000003764	6 retrocopies	retro_dord_25, retro_dord_290, retro_dord_599, retro_dord_64, retro_dord_647, retro_dord_739,
Equus caballus	ENSECAG00000003460	1 retrocopy	retro_ecab_975,
Echinops telfairi	ENSETEG00000003337	4 retrocopies	retro_etel_1246, retro_etel_1938, retro_etel_239, retro_etel_497,
Felis catus	ENSFCAG00000001347	1 retrocopy	retro_fcat_1041,
Homo sapiens	ENSG00000173207	1 retrocopy	retro_hsap_27,
Gorilla gorilla	ENSGGOG00000013419	4 retrocopies	retro_ggor_10, retro_ggor_1070, retro_ggor_2739, retro_ggor_659,
Loxodonta africana	ENSLAFG00000032213	1 retrocopy	retro_lafr_243,
Mus musculus	ENSMUSG00000028044	1 retrocopy	retro_mmus_280 ,
Mus musculus	ENSMUSG00000062248	4 retrocopies	retro_mmus_1356, retro_mmus_1470, retro_mmus_2392, retro_mmus_409,
Nomascus leucogenys	ENSNLEG00000011532	3 retrocopies	retro_nleu_1098, retro_nleu_2592, retro_nleu_411,
Oryctolagus cuniculus	ENSOCUG00000016204	2 retrocopies	retro_ocun_1389, retro_ocun_18,
Otolemur garnettii	ENSOGAG00000006384	10 retrocopies	retro_ogar_1673, retro_ogar_1703, retro_ogar_1713, retro_ogar_1983, retro_ogar_2317, retro_ogar_245, retro_ogar_3310, retro_ogar_450, retro_ogar_530, retro_ogar_877,
Pongo abelii	ENSPPYG00000000768	3 retrocopies	retro_pabe_1143, retro_pabe_3625, retro_pabe_717,
Pan troglodytes	ENSPTRG00000001398	4 retrocopies	retro_ptro_2769, retro_ptro_3100, retro_ptro_558, retro_ptro_944,
Rattus norvegicus	ENSRNOG00000042561	1 retrocopy	retro_rnor_97,
Sorex araneus	ENSSARG00000012383	2 retrocopies	retro_sara_667, retro_sara_77,
Sus scrofa	ENSSSCG00000029737	1 retrocopy	retro_sscr_730,
Vicugna pacos	ENSVPAG00000012182	1 retrocopy	retro_vpac_532,